Fisheries play a crucial role in global nutrition, economic stability, and ecosystem conservation, with approximately three billion people relying on seafood as their primary protein source. However, the sustainability of fisheries faces increasing threats such as overexploitation, habitat loss, pollution, and climate change. To address these challenges, fisheries research has become essential, encompassing various scientific inquiries from fish population biology and ecology to the socioeconomic aspects of fishing communities. Next-generation sequencing (NGS) technologies have revolutionized the field of fishery science, offering novel research possibilities, and have become instrumental in the conservation, management, and sustainability of aquatic resources. NGS enables the sequencing of complete genomes, transcriptomes, and environmental DNA with remarkable precision and speed, transforming traditional genetic research. This chapter explores the applications of NGS in fisheries research, highlighting its impact and potential in addressing the challenges facing aquatic ecosystems.